Pokemon Ninja
by RandomGuy26
Summary: What if Naruto was given the tools for success? He becomes the first Poke Nin. NarutoxMabui.


**Hello, everyone. This is my first story and I'm going to do my best on it. If there is anything wrong or not explained, please PM me. I do not own Naruto or Pokémon.**

It was very dark.

That's all Naruto could distinguish when he had blacked out. Mizuki revealing that he was the container of the Kyuubi no Yoko had put him in shock. That didn't help when the traitor had thrown kunai and shuriken at him.

Like any one, he was going to try to dodge. For some reason he had blacked out before he could make his first step. Naruto believed he was most likely dead.

"You're not dead yet, boy." The boy blinked before turning around.

Instead of a human figure he had expected, it was just a bright light with a figure inside. No indication was shown that it had spoken, but he knew something was in there. The power was so intense.

"Who are you?" Naruto asked warily. The light seemed to become brighter.

"**My name is Arcues, Child of the Prophecy. I am the creator of the Pokémon world and I helped shaped the universe."** The boy backed up a little bit in alarm.

"Are you Kami then?" Arcues chuckled in amusement which made Naruto a bit irritated.

"**No I am not Kami. Kami created the universe and its inhabitants which was me and a few others. While Kami could have shaped the universe, she gave the job to us. Creating Pokémon was something I did to help out humans with things beyond their capability; although my abilities are considered godlike."**

"What's Pokémon, Arcues-sama?"

"**The creatures themselves, based on various plants, animals, and other concepts, use to inhabit virtually every corner of the world. Many would make their homes in forests and on rural routes stretching across the various regions, while still others were native to cities and other urban centers. There were 649 known Pokémon. Pokémon that were owned by a person were kept in Poké Balls, which allowed for them to be quickly sent into battle or to perform a task, but kept them safe and make them easier to transport. Many Pokémon owned by Trainers, however, chose to remain outside of their Poké Ball, and travel with their Trainer on foot. Pokémon began their lives by hatching from eggs, and many of them will evolve to grow stronger and larger during the course of their lives. Pokémon far surpass those of normal animals. Each was able to create an element or control something. Some even had ghost-like abilities."**

Naruto was amazed at the beings. They seemed to be like shinobi.

"You were talking in past-tense. Did something happen to them?" Killer intent flooded the area, making it harder to breathe for the blond.

"**The humans started to see Pokémon as threats or weapons. They started to making ways to capture Pokémon with Poke Balls. Then they started to use them for their own sick methods, like war. This had caused the Pokémon population to decrease severely. The Pokémon had to go into hiding to avoid unnecessary death, but they could only hide for so long. So The Legendary Pokémon began to join the fight too. We began to kill of humans to show them the consequences of their actions, but I was not pleased. I wanted to end the human race and finish what they started."**

"Wait, if you wanted to end our race then why are we still here?" Arcues sighed.

"**There was a man named Ash Ketchum, your descendant. He was a very skilled Pokémon trainer who was able to gain favor from even The Legendaries. You see, he led a group in secret that opposed the use of the Pokémon. He and a few others would try to end the pointless war, but their numbers weren't enough. The man knew I had the ability to end it all, but he wanted to spare the humans. So he had confronted me and begged me to end it. He had gained my favor before, so I trusted him."**

"What happened after that?" Naruto was so curious. He wondered why no one spoke of these creatures.

"**I made everyone forget that Pokémon ever existed. Even though they forgot Pokémon ever existed, they somehow remembered thier techniques. They developed fighting styles because of this. They also developed the ability to use lightning, water, fire, and ground attacks. Some blood-lines revolve around some of the other elements like Ice."**

"So that's what started the Shinobi system?"

"**No, it's not. You see, some of my plates, which allows me to control an element, was missing. A human had found them and merged with them. The plates were for ghost, bug, steel, flying, poison, and dark type Pokémon. Most of these plates were incompatible for the human. It had turned him into a monster known as the Juubi, a monster that no mortal was able to defeat."**

"How was it defeated then? I never heard of this monster. The only ones I know of are the Biju."

"**A man known as the Rikudo Sennin came along. His mastery at using the elements was beyond even Pokémon standards by using the anceint energy Aura or as you humans called chakra. He decided to call it Ninjutsu. He also dissected a Poke ball and created Fuinjutsu, the art of sealing. With his knowledge of Fuinjutsu, he sealed the Juubi in himself increasing his power by leaps and bounds."**

Naruto was in awe of the Rikudo Sennin. To think he was to tame a beast even stronger than the Biju! It was far beyond the power of even the Fourth Hokage!

"What happened to the Sage?"

"**Although he had successfully sealed the Ten-Tails, its power was so great that the seal would break after the Sage's death. Aware of this, the Sage used another one of his abilities to divide the Ten-Tails' chakra into nine parts, which would become known as the Biju. He sealed the monster inside the moon."**

"Wow." Was all Naruto could use to describe the story.

"**That's not what I called you here for." **Six Poke Balls, a red device, and some gloves appeared in front of him. **"Like Ash Ketchum, you are destined to change this world, for better or worst. We think you would do best with Pokémon of your own. Those Poke Balls are filled with Pokémon in their pre-evolved form, except for one. Right, now most of them are weak and do not have many moves."**

Naruto was jumping up and down at the prospect of having his first friends.

"**The red device is called a PokeDex. It will help you identify Pokémon that you might encounter. If you scan a Pokémon while it's doing a move, then you can perform it too. Since you are in danger, I put in Focus Punch and Aura Sphere. To perfect the moves will require practice, but they will be helpful in case you don't have a Pokémon with you."**

"**The gloves are the gloves of an Aura Guardian. Those gloves will help you control your chakra. While wearing these gloves, you can perform Ninjutsu or use Aura without it draining your reserves. This overcomes the Jinchuriki poor control."**

Naruto was almost crying. He had never received so many gifts at once. Naruto started to disappear in a shower of silver sparkles.

"Thank you." The light flickered in response.

"**No problem... Naruto Uzumaki"**

…**.**

When Naruto opened his eyes, he saw that everything was frozen. Nothing was moving an inch. He saw than the weapons were almost a foot away from him. Mizuki had a sneer on his face, while staring at him. Iruka seemed to be trying to run towards him with a panicked expression on his face.

"_**Move you dimwit!"**_ The blonde jumped up as time started again. The weapons launched into the tree and Iruka tackling him to the ground.

"What the hell, sensei!" The blonde shouted.

"Huh, are you ok, Naruto?" The man asked his student. He didn't expect Naruto to dodge the fast projectiles.

"Don't you ignore me!" Mizuki yelled as he threw his Fūma Shuriken at the duo.

Iruka looked up in alarm. He had doubted that he could get both him AND Naruto out of the way but he could try. He looked down to see his student with some gloves on his hands when suddenly a ball of blue chakra emerged from the palm of his hands.

'_Such power and control! He compressed his chakra into one point making it shape like a ball. Whatever it hits will surely break, just like the Fourth's famous __**Rasengan**__. Naruto… how strong have you become?"_

"**Aura Sphere!" **The ball flew towards Mizuki and in the process broke the Fūma Shuriken. The men eyes widened at the power, before the ball hit Mizuki in the chest.

It started to grind into him a little bit before he was propelled into the forest. (Like the Rainbow Rasengan results.) Iruka could only gape at the destruction of the technique.

"Naruto, how did you learn such a technique?" The blonde turned towards him and smiled. He noticed Naruto's eyes were glowing slightly.

"I guess I was always able to do it. Now let's go take you to the hospital."

…

Naruto sighed as he stood in the middle of a training field. He had talked to the Hokage and there was a three moth interval between graduation and team placements. So he had to train his new Pokémon to be topnotch by that time. He could get a little bit of training in too.

"Alright! Time to see what kind of Pokémon you guys are! Come on out!" The boy threw up all six of his Poke balls and red light came from them.

What Naruto expected to come out was totally bad-ass creatures. The Pokémon that came out was _cute._

The cutest one there is a rodent. Its fur is very short, and it is pale yellow in color. The tips of its large ears are black, and it has additional black markings on its neck and tail. Its tail is short, but still bears some resemblance to the large lightning-bolt structure. It has pouches in its cheeks, which are pinkish colored and its nose is extremely small, almost like a dot. Naruto took out his PokeDex.

"_Pichu, the Tiny Mouse Pokémon. The pre-evolved form of Pikachu. Despite their size, Pichu release bursts of electricity that can shock even humans. However, Pichu are unskilled at controlling their electricity, and sometimes release it by accident when surprised or when laughing and shock themselves__."_

The next one had short, orange-brown fur that covers its body, except for the mouth and the crescent moon marking on its head, which has a light tan. It has a small, round body with short limbs and a short, puffy tail and has circular eyes with blue irises, three claws on its forepaws.

"_Teddiursa, the Little Bear Pokémon. This cute, cuddly Pokémon is easily frightened and frequently licks its paws, which are usually covered with sweet honey."_

One of the other Pokémon was baby seal-like. Its plushy fur is a powdered blue color, with several white spots on its back and a beige underside. It has circular eyes, small tusks protruding from the upper jaw, stubby ears, beige flippers and a little flat tail. For some reason, it resembles a ball.

"_Spheal, the Clap Pokémon. Spheal moves more quickly by rolling than by walking. They are sometimes known to cross oceans atop icebergs."_

The next one made him shiver. It had a purple flame on top its head. Its body is made up primarily of white wax. The folded, melted wax lies over its right eye, and leaves only the bright yellow left eye visible. It has a small smile.

"_Litwick, the Candle Pokémon. It shines a light that absorbs the life energy of people and Pokémon, which becomes the fuel that it burns_."

Out of all the Pokémon, the last two looked awesome. One was a small, blue, dog-like Pokémon. Its legs and torso are colored black. The tail is blue and it has a yellow collar. There are rounded bumps on the backs of its forepaws. It also has a black "mask" and red eyes and stands on its toes instead of its entire foot.

"_Riolu, the Emanation Pokémon. When sad or scared, Riolu's aura becomes stronger as a way of signaling its allies"_

The last one was possibly the strongest because of the energy it was producing. It is a bird-like dragon Pokémon. The lower half of its body is blue with jet-plane wings and stubby feet. It has a red triangle-shaped ring on its chest. The upper-half of its body is white. It has triangle-shaped ears and a blue face with a white pentagon in the middle.

"_Latios, the Jet Pokémon. Latios is__ a highly intelligent Pokémon. By folding back its wings in flight, it can overtake jet planes."_

'_Master, are you alright?'_ Naruto jumped in shocked and noticed his Pokémon was staring at him with worried expressions. He had to guess Latios said that since he was a physic type.

"Yeah, I'm fine. I guess I was expected something different." Pichu ran up towards Naruto and jumped on his head.

"Pichu pi pichu!" Pichu looked at him with curiosity.

"We're going to be training for three months. I am going to make sure you guys are tough enough to survive this world and be able to support each other abilities. You guys ready to start!" The smaller Pokémon squealed in happiness while Latios smiled.

**That's it. I hoped you enjoyed the first chapter. The next chapter will show that some of Naruto's Pokémon had evolved during training. If you want Naruto to catch a Pokémon please tell me in a review. It will be a long time before that happens though.( No Legendary Pokémon) **


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